GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlG in Herbaspirillum seropedicae SmR1

Align ABC transporter for D-Sorbitol, permease component 1 (characterized)
to candidate HSERO_RS16730 HSERO_RS16730 sugar ABC transporter permease

Query= reanno::acidovorax_3H11:Ac3H11_2942
         (279 letters)



>FitnessBrowser__HerbieS:HSERO_RS16730
          Length = 293

 Score =  137 bits (346), Expect = 2e-37
 Identities = 82/257 (31%), Positives = 139/257 (54%), Gaps = 5/257 (1%)

Query: 27  LLFFPLGWLFLTAFK--TELQAIAVPPLFVFTPTLENFHEVQERSDYLLYAKNSVITSVL 84
           +L FP  W+ +TAFK   EL + +  P +V  PTL +F ++   + Y  +  N+VI SV+
Sbjct: 37  VLLFPFYWMVITAFKPDNELLSQSGNPFWVIAPTLAHFKKLLFDTQYPAWLLNTVIVSVV 96

Query: 85  STVLGLMLAAPAAYAMAFFKGKYTKDILMWMLSTKMMPAVGALVPIYVLAQKSHLLDTQL 144
           ST   L  +  AAYA+   + + +K + + +    ++P     +P+  +  K  L DT+ 
Sbjct: 97  STFASLAASVFAAYAIERLRFQGSKQVGLGIFLAYLIPPSILFIPLAAIVFKLGLFDTRW 156

Query: 145 ALIIVFALSNLPIMVWMLYSHFKDIPHEILEAARMDGATLWQEVRLVLLPLGMGGLASTG 204
           ALI+ +    +P   W+L  +F+ IP+E+ E A +DGAT W+ +  ++LPL + GL S G
Sbjct: 157 ALILTYPTFLIPFCTWLLMGYFRSIPYELEECALIDGATRWEILVKIILPLAVPGLISAG 216

Query: 205 LLCLVLSWNEAFWSLN-LSAAKAGTLAT-LIASYSSPEGLFWAKLSAASLMAIAPIVVFG 262
           +    LSWNE  ++L  +S+++  T+   ++      +   W  L A +L+   P+ V  
Sbjct: 217 IFAFTLSWNEFIYALTFISSSEVKTVPVGIVTELVEGDVYHWGALMAGALLGSLPVAVVY 276

Query: 263 WFSQKQLVQGLTFGAVK 279
            F  +  V G+T GAVK
Sbjct: 277 SFFVEYYVSGMT-GAVK 292


Lambda     K      H
   0.327    0.137    0.420 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 218
Number of extensions: 6
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 279
Length of database: 293
Length adjustment: 26
Effective length of query: 253
Effective length of database: 267
Effective search space:    67551
Effective search space used:    67551
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory